SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Remove reads which are not uniquely mapped hanleng Bioinformatics 9 08-25-2015 05:04 AM
Bowtie1 for ChIP-seq: uniquely mapped reads with up to two mismatches Jerry_Zhao Bioinformatics 0 01-21-2014 07:28 AM
uniquely mapped reads Carmen Bioinformatics 8 12-14-2012 05:01 AM
not uniquely mapped reads unidodo RNA Sequencing 2 04-22-2011 02:07 PM
Uniquely mapped reads with bowtie mapper Bioinformatics 2 11-22-2010 10:44 PM

Reply
 
Thread Tools
Old 01-30-2020, 05:47 AM   #1
Hedi86
Member
 
Location: Norway

Join Date: Oct 2017
Posts: 23
Default length of uniquely mapped seq in Bismark

Dear all

Bismark reports the number of allignments with a unique best hit, is there a way to know what was the Length of those unique sequences ? for instance I have an RRBS library which after trimming has seq length of 20 - 140 bp, this gave me about 40% unique mapping in Bismark, I would like to know the length of those fragments which mapped uniquely.

Best regards
Hedi86 is offline   Reply With Quote
Old 01-31-2020, 12:54 AM   #2
fkrueger
Senior Member
 
Location: Cambridge, UK

Join Date: Sep 2009
Posts: 622
Default

Hi Hedi,

Every alignment that is reported by Bismark are unique hits (ambiguosly aligning reads are discarded, and not-aligning reads - well - don't align at all). So you can simply look at the aligned read length distribution using your program of choice. It would only be 2 clicks in SeqMonk for example. As a general rule though, longer reads tend to align better.

40% mapping efficiency doesn't sound great to be honest. Which organisma are you working with, and did you perform appropriate adapter/quality trimming etc?
fkrueger is offline   Reply With Quote
Old 01-31-2020, 03:57 AM   #3
Hedi86
Member
 
Location: Norway

Join Date: Oct 2017
Posts: 23
Default

thank you Felix

so i just imported the BAM files generated by Bismark into Seqmonk, without any quantification i can click on read length distribution histogram on data sets. but trimmed files should have 20 - 140 bp length, why still i can see seq with for example 400 bp in BAM files?

we are working with bull data, and yes we did pay attention to evrything when it comes to trimming and quality assessment. but still this is what we have unfortunatelly.

Appreciate your halp
Hedi86 is offline   Reply With Quote
Old 01-31-2020, 04:00 AM   #4
fkrueger
Senior Member
 
Location: Cambridge, UK

Join Date: Sep 2009
Posts: 622
Default

That sounds like you are working with paired-end data. In that case the Read 1 and Read 2 will be ends of the fragment you are sequencing, and they may well be further apart. In this case it doesn't really matter how long each read is, but it is the combination of the mappability of R1 and R2 that counts.
fkrueger is offline   Reply With Quote
Old 01-31-2020, 04:26 AM   #5
Hedi86
Member
 
Location: Norway

Join Date: Oct 2017
Posts: 23
Default

thank you

we actually used two different kits for RRBS library preparation, I figured out that there is lots of short reads under 70 bp in the first method and using another method the peak of read length was about 130 bp which we would like to have, as you mentioned longer reads tend to align better. but surprisingly mapping was almost the same, that's why i was curious to look at the length of those aligned reads in both libraries.

Best
Hedi86 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:14 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO